A role for genomics-based studies of Bordetella pertussis adaptation.

Purpose of review: Cases of whooping cough (pertussis) have rebounded strongly from the very low incidence observed during the pandemic. This re-emergence is characterized by changes in epidemiology. Here we describe the importance of genomics to monitor and understand the drivers to these changes. 

Recent findings: Changes in the genotype of strains isolated during recent outbreaks suggests that the pandemic disturbed the global Bordetella pertussis population structure. The emergence of dominant and antibiotic-resistant clones in China is of concern even though the source of antibiotic selection pressure on B. pertussis is unclear. A recent study illustrates how to use genomic data to go beyond just surveillance, inferring the relative fitness of genotypes and the identification of specific mutations distinguishing such lineages. Such approaches are required to understand the forces driving adaptation. 

Summary: Pertussis is resurgent in many countries, involving changes in epidemiology and strong suggestions of strain adaptation. The continued use of vaccination, and design of new interventions, to control pertussis requires an understanding of these changes. Genomic analyses will be key to this, involving integration of more complete host and pathogen parameters than have been used to date.